Package schrodinger :: Module structure :: Class _Residue

Class _Residue

_AtomCollection --+
                  |
                 _Residue

A class which is returned by the ResidueIterator and contains information about the residue including the atoms which make it up.

Important methods include extractStructure and getAtomList. The atom attribute can be used to iterate over all atoms in the molecule, and the number of atoms can be determined via len(molecule.atom).

Instance Methods

[hide private]

__init__(self, st, resnum, inscode, chain, atoms=[])

__str__(self)
Return a string representation - chain:resnum[inscode].

_getPdbRes(self)

_setPdbRes(self, newvalue)

_getChain(self)

_setChain(self, newvalue)

_getResnum(self)

_setResnum(self, newvalue)

_getInscode(self)

_setInscode(self, newvalue)

_getBF(self)

_getMolNumber(self)

_getSecStruct(self)

getCode(self)
Return the one-letter residue code for this residue.

hasMissingAtoms(self)
Returns True is this residue doesn't have the expected number of heavy atoms.

isStandardResidue(self)
Returns True if this residue is on the list of standard PDB residues

isConnectedToResidue(self, other_res)
Returns True if the given residue is connected (C->N) to this residue.

applyStyle(self, atoms=ATOM_BALLNSTICK, bonds=BOND_BALLNSTICK)
Applies the given display styles to the atoms and bonds of the residue.

Inherited from _AtomCollection: __len__, atom, extractStructure, getAtomList

Class Variables

[hide private]

pdbres = property(_getPdbRes, _setPdbRes, doc= "PDB residue na...

chain = property(_getChain, _setChain, doc= "Chain name")

resnum = property(_getResnum, _setResnum, doc= "PDB residue nu...

inscode = property(_getInscode, _setInscode, doc= "PDB residue...

temperature_factor = property(_getBF, doc= "Residue B (tempera...

molecule_number = property(_getMolNumber, doc= "Molecule number")

secondary_structure = property(_getSecStruct, doc= "Secondary ...

Method Details

[hide private]

init(self, st, resnum, inscode, chain, atoms=[])
(Constructor)

Overrides: _AtomCollection.__init__

str(self)
(Informal representation operator)

Return a string representation - chain:resnum[inscode]. Insertion code is included only it is present. If the residue has no chain ID, then underscore ("_") is used.

hasMissingAtoms(self)

Returns True is this residue doesn't have the expected number of heavy atoms. Will return False is this residue has the correct number of heavy atoms or if it is of a type we don't know

isConnectedToResidue(self, other_res)

Returns True if the given residue is connected (C->N) to this residue.

If the "C" PDB atom of this residue is connected to the "N" PDB atom of the other_res, then the residues are connected. Otherwise, they are not considered connected.

applyStyle(self, atoms=ATOM_BALLNSTICK, bonds=BOND_BALLNSTICK)

Applies the given display styles to the atoms and bonds of the residue.

Parameters:

atoms (int) - display style for atoms given by structure module constants ATOM_NOSTYLE, ATOM_CIRCLE, ATOM_CPK, ATOM_BALLNSTICK. Default is ATOM_BALLNSTICK.
atoms (int) - display style for bonds given by structure module constants BOND_NOSTYLE, BOND_WIRE, BOND_TUBE, BOND_BALLNSTICK. Default is BOND_BALLNSTICK.
bonds (int)

Class Variable Details

[hide private]

pdbres

Value:

property(_getPdbRes, _setPdbRes, doc= "PDB residue name")

resnum

Value:

property(_getResnum, _setResnum, doc= "PDB residue number")

inscode

Value:

property(_getInscode, _setInscode, doc= "PDB residue insertion code")

temperature_factor

Value:

property(_getBF, doc= "Residue B (temperature) factor")

secondary_structure

Value:

property(_getSecStruct, doc= "Secondary structure")

Class _Residue

__init__(self, st, resnum, inscode, chain, atoms=[]) (Constructor)

__str__(self) (Informal representation operator)

hasMissingAtoms(self)

isConnectedToResidue(self, other_res)

applyStyle(self, atoms=ATOM_BALLNSTICK, bonds=BOND_BALLNSTICK)

pdbres

resnum

inscode

temperature_factor

secondary_structure

init(self, st, resnum, inscode, chain, atoms=[])
(Constructor)

str(self)
(Informal representation operator)